update jsbmlReader call

met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/attributes/ExtractPathways.java

@@ -35,7 +35,7 @@ public class ExtractPathways extends AbstractMet4jApplication {
 
     public void run() throws IOException, Met4jSbmlReaderException, Met4jSbmlWriterException {
         //read smbl
-        JsbmlReader reader = new JsbmlReader(this.inputPath, false);
+        JsbmlReader reader = new JsbmlReader(this.inputPath);
         BioNetwork network = reader.read();
         System.out.println("Number of reactions in original network: "+network.getReactionsView().size());
         System.out.println("Number of species in original network: "+network.getMetabolitesView().size());

met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/attributes/ExtractSbmlAnnot.java

@@ -53,7 +53,7 @@ public class ExtractSbmlAnnot extends AbstractMet4jApplication {
         FileWriter fw = new FileWriter(outputPath);
 
         //read smbl
-        JsbmlReader reader = new JsbmlReader(this.inputPath, true);
+        JsbmlReader reader = new JsbmlReader(this.inputPath);
         BioNetwork network = reader.read();
 
         BioCollection<? extends BioEntity> entities = new BioCollection<>();